Align glycerol-3-phosphate dehydrogenase; EC 1.1.5.3 (characterized)
to candidate N515DRAFT_3909 N515DRAFT_3909 homodimeric glycerol 3-phosphate dehydrogenase (quinone) (EC 1.1.5.3)
Query= CharProtDB::CH_091834 (512 letters) >FitnessBrowser__Dyella79:N515DRAFT_3909 Length = 499 Score = 535 bits (1377), Expect = e-156 Identities = 282/493 (57%), Positives = 340/493 (68%), Gaps = 7/493 (1%) Query: 11 LAEVYDVAVVGGGINGVGIAADAAGRGLSVFLCEQHDLAQHTSSASSKLIHGGLRYLEHY 70 + E DV VVGGGING GIA DA GRGLSV+LCEQ DLA HTSSAS+KLIHGGLRYLE + Sbjct: 1 MTEQVDVLVVGGGINGTGIARDAVGRGLSVWLCEQDDLASHTSSASTKLIHGGLRYLEQF 60 Query: 71 EFRLVREALAEREVLLAKAPHIVKPLRFVLPHRPHLRPAWMIRAGLFLYDHLGK-REKLP 129 EF LV +ALAERE+LL APHI+ PLRFVLPH+ HLRPAWMIR GLFLYDHL + R LP Sbjct: 61 EFALVGKALAEREILLRVAPHIIWPLRFVLPHQSHLRPAWMIRLGLFLYDHLQRGRRSLP 120 Query: 130 ASRGLRFTGSS---PLKAEIRRGFEYSDCAVDDARLVVLNAISAREHGAHVHTRTRCVSA 186 SR +R + + PL+ E GF YSD V DARLVVLNA+ A + GA V T TRCVSA Sbjct: 121 GSRRVRLSRHAVGQPLRDEFPIGFVYSDAWVQDARLVVLNAMDAVQRGARVMTHTRCVSA 180 Query: 187 RRSKGLWHLHLERSDGSLYSIRARALVNAAGPWVARFIQDDLKQKSPYGIRLIQGSHIIV 246 RRS W L+ S+G + + ARALVNA GPW F+ + + +G+RL++GSHI+V Sbjct: 181 RRSGERWLARLQSSNGQVTEVAARALVNATGPWAVDFLDEVAAEGHDHGLRLVKGSHIVV 240 Query: 247 PKLYEGEHAYILQNEDRRIVFAIPYLDRFTMIGTTDREYQGDPAKVAISEEETAYLLQVV 306 P+LY+ +AYI Q DRRIVFAIPY FT+IGTTD EY+GDPA I +ETAYL V Sbjct: 241 PRLYDHRYAYIFQQPDRRIVFAIPYEREFTLIGTTDVEYRGDPAHPRIDTQETAYLCDAV 300 Query: 307 NAHFKQQLAAADILHSFAGVRPLCDDESDEPSAITRDYTLSLSAGNGEPPLLSVFGGKLT 366 N +FK+ + AD++ S++GVRPL DD+S + S +TRDY L L G PLL+VFGGKLT Sbjct: 301 NRYFKRGIVPADVVWSYSGVRPLLDDDSGKASEVTRDYLLELEQARG-APLLNVFGGKLT 359 Query: 367 TYRKLAESALTQLQPFFANLGPAWTAKA-PLPGGEQMQSVEALTEQLANRYAWLDRELAL 425 T+RKLAE A+ +L P N PAWT K PLPGG+ +Q L EQL WL +A Sbjct: 360 TFRKLAEEAVDRLAPLLGNREPAWTGKGHPLPGGD-IQDPGRLAEQLRATRPWLGEAMAW 418 Query: 426 RWARTYGTRVWRLLDGVNGEADLGEHLGGGLYAREVDYLCKHEWAQDAEDILWRRSKLGL 485 R A TYG++ R+L LGEH G LYA EVDYL ++EWA AED+LWRR+KLGL Sbjct: 419 RLAHTYGSQSVRVLGDAASLTGLGEHFGADLYASEVDYLRRYEWAGSAEDVLWRRTKLGL 478 Query: 486 FLSPSQQVRLGQY 498 + RL Y Sbjct: 479 HIGGEGAARLAAY 491 Lambda K H 0.321 0.136 0.415 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 792 Number of extensions: 42 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 512 Length of database: 499 Length adjustment: 34 Effective length of query: 478 Effective length of database: 465 Effective search space: 222270 Effective search space used: 222270 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory